Starting phenix.real_space_refine on Wed Jul 23 10:57:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.map" model { file = "/net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gsb_34228/07_2025/8gsb_34228.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2001 2.51 5 N 544 2.21 5 O 596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1404 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 3.38, per 1000 atoms: 1.07 Number of scatterers: 3157 At special positions: 0 Unit cell: (78.306, 60.624, 95.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 596 8.00 N 544 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 414.0 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.2% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.238A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.632A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.527A pdb=" N THR K 66 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.456A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1010 1.34 - 1.46: 819 1.46 - 1.58: 1389 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3237 Sorted by residual: bond pdb=" C PRO K 81 " pdb=" N GLU K 82 " ideal model delta sigma weight residual 1.334 1.280 0.054 1.38e-02 5.25e+03 1.54e+01 bond pdb=" C LEU K 74 " pdb=" N THR K 75 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.55e-02 4.16e+03 1.33e+01 bond pdb=" C GLN K 90 " pdb=" N GLN K 91 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.39e-02 5.18e+03 1.19e+01 bond pdb=" C ALA A 419 " pdb=" N ASP A 420 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.51e-02 4.39e+03 8.15e+00 bond pdb=" C GLU H 46 " pdb=" N TRP H 47 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.31e-02 5.83e+03 7.24e+00 ... (remaining 3232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 4246 1.78 - 3.57: 125 3.57 - 5.35: 17 5.35 - 7.14: 2 7.14 - 8.92: 4 Bond angle restraints: 4394 Sorted by residual: angle pdb=" N GLN K 91 " pdb=" CA GLN K 91 " pdb=" C GLN K 91 " ideal model delta sigma weight residual 109.24 100.32 8.92 1.63e+00 3.76e-01 3.00e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 109.34 117.51 -8.17 2.08e+00 2.31e-01 1.54e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.18 104.87 8.31 2.37e+00 1.78e-01 1.23e+01 angle pdb=" N PHE A 400 " pdb=" CA PHE A 400 " pdb=" C PHE A 400 " ideal model delta sigma weight residual 108.99 114.35 -5.36 1.57e+00 4.06e-01 1.17e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1655 14.28 - 28.56: 186 28.56 - 42.85: 46 42.85 - 57.13: 16 57.13 - 71.41: 4 Dihedral angle restraints: 1907 sinusoidal: 752 harmonic: 1155 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.88 -61.88 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CA ALA A 475 " pdb=" C ALA A 475 " pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " pdb=" SG CYS H 106 " pdb=" CB CYS H 106 " ideal model delta sinusoidal sigma weight residual 93.00 133.22 -40.22 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 1904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 385 0.052 - 0.104: 61 0.104 - 0.156: 20 0.156 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA GLN A 474 " pdb=" N GLN A 474 " pdb=" C GLN A 474 " pdb=" CB GLN A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL H 119 " pdb=" N VAL H 119 " pdb=" C VAL H 119 " pdb=" CB VAL H 119 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 464 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 44 " -0.181 9.50e-02 1.11e+02 8.12e-02 4.43e+00 pdb=" NE ARG H 44 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 44 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 44 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 44 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO K 8 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 492 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C LEU A 492 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 492 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 493 " 0.011 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1168 2.85 - 3.36: 2819 3.36 - 3.88: 4750 3.88 - 4.39: 5283 4.39 - 4.90: 9213 Nonbonded interactions: 23233 Sorted by model distance: nonbonded pdb=" O GLY H 26 " pdb=" OG1 THR H 30 " model vdw 2.338 3.040 nonbonded pdb=" O GLN A 474 " pdb=" O ASN A 487 " model vdw 2.372 3.040 nonbonded pdb=" O SER A 514 " pdb=" OG SER A 514 " model vdw 2.395 3.040 nonbonded pdb=" O ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.406 3.040 nonbonded pdb=" O ASP A 339 " pdb=" OD1 ASP A 339 " model vdw 2.414 3.040 ... (remaining 23228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3242 Z= 0.245 Angle : 0.728 8.922 4404 Z= 0.429 Chirality : 0.045 0.259 467 Planarity : 0.005 0.081 569 Dihedral : 13.337 71.409 1158 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.42), residues: 392 helix: -3.19 (1.17), residues: 8 sheet: -0.89 (0.49), residues: 119 loop : -1.36 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 97 HIS 0.001 0.001 HIS A 505 PHE 0.011 0.001 PHE A 486 TYR 0.027 0.002 TYR K 92 ARG 0.011 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.26585 ( 80) hydrogen bonds : angle 9.55811 ( 204) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.80340 ( 10) covalent geometry : bond 0.00396 ( 3237) covalent geometry : angle 0.72832 ( 4394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.339 Fit side-chains REVERT: A 474 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6603 (tp-100) REVERT: H 47 TRP cc_start: 0.8813 (t60) cc_final: 0.8193 (t60) REVERT: K 8 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: K 33 TYR cc_start: 0.7996 (m-10) cc_final: 0.7765 (m-10) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2199 time to fit residues: 19.3063 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105412 restraints weight = 6555.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106450 restraints weight = 5158.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107393 restraints weight = 4686.155| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3242 Z= 0.143 Angle : 0.623 8.899 4404 Z= 0.330 Chirality : 0.044 0.137 467 Planarity : 0.004 0.041 569 Dihedral : 4.880 24.389 447 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.46 % Allowed : 9.33 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.42), residues: 392 helix: -3.11 (1.45), residues: 8 sheet: -0.70 (0.48), residues: 126 loop : -1.06 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 97 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.002 PHE A 486 TYR 0.027 0.002 TYR K 92 ARG 0.005 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 80) hydrogen bonds : angle 6.57563 ( 204) SS BOND : bond 0.00290 ( 5) SS BOND : angle 1.07658 ( 10) covalent geometry : bond 0.00333 ( 3237) covalent geometry : angle 0.62178 ( 4394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8237 (m-30) cc_final: 0.7939 (t0) REVERT: H 47 TRP cc_start: 0.8790 (t60) cc_final: 0.8319 (t60) REVERT: H 57 ASN cc_start: 0.8297 (t0) cc_final: 0.7871 (t0) outliers start: 5 outliers final: 1 residues processed: 79 average time/residue: 0.2269 time to fit residues: 20.5466 Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101460 restraints weight = 6648.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101292 restraints weight = 5299.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101841 restraints weight = 5923.103| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3242 Z= 0.189 Angle : 0.626 8.147 4404 Z= 0.334 Chirality : 0.045 0.147 467 Planarity : 0.005 0.038 569 Dihedral : 5.103 24.745 447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.33 % Allowed : 11.95 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.41), residues: 392 helix: -4.25 (0.80), residues: 15 sheet: -0.78 (0.46), residues: 128 loop : -1.08 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.002 PHE A 400 TYR 0.032 0.002 TYR K 92 ARG 0.008 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 80) hydrogen bonds : angle 5.96403 ( 204) SS BOND : bond 0.00248 ( 5) SS BOND : angle 1.16019 ( 10) covalent geometry : bond 0.00449 ( 3237) covalent geometry : angle 0.62432 ( 4394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8379 (m-30) cc_final: 0.8110 (m-30) REVERT: A 442 ASP cc_start: 0.8279 (m-30) cc_final: 0.8035 (t0) REVERT: H 47 TRP cc_start: 0.8953 (t60) cc_final: 0.8533 (t60) REVERT: H 57 ASN cc_start: 0.8411 (t0) cc_final: 0.8082 (t0) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.2118 time to fit residues: 17.2726 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099479 restraints weight = 6639.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099933 restraints weight = 5532.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100596 restraints weight = 6008.579| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3242 Z= 0.270 Angle : 0.691 8.654 4404 Z= 0.369 Chirality : 0.046 0.147 467 Planarity : 0.005 0.037 569 Dihedral : 5.569 24.142 447 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.08 % Allowed : 13.99 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.41), residues: 392 helix: -4.19 (0.84), residues: 14 sheet: -1.04 (0.45), residues: 129 loop : -1.24 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 36 HIS 0.002 0.001 HIS H 100 PHE 0.020 0.002 PHE A 400 TYR 0.028 0.002 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 80) hydrogen bonds : angle 5.85640 ( 204) SS BOND : bond 0.00284 ( 5) SS BOND : angle 1.28001 ( 10) covalent geometry : bond 0.00645 ( 3237) covalent geometry : angle 0.68917 ( 4394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.383 Fit side-chains REVERT: A 405 ASP cc_start: 0.8375 (m-30) cc_final: 0.8021 (m-30) REVERT: A 442 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8136 (t0) REVERT: A 474 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7497 (tm-30) REVERT: H 57 ASN cc_start: 0.8473 (t0) cc_final: 0.8203 (t0) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.2026 time to fit residues: 17.0580 Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103263 restraints weight = 6565.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102891 restraints weight = 5296.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103887 restraints weight = 5649.098| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3242 Z= 0.121 Angle : 0.597 8.640 4404 Z= 0.313 Chirality : 0.043 0.132 467 Planarity : 0.004 0.038 569 Dihedral : 4.936 24.772 447 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.92 % Allowed : 15.16 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.41), residues: 392 helix: -4.21 (0.90), residues: 15 sheet: -0.83 (0.45), residues: 129 loop : -1.12 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 392 TYR 0.019 0.001 TYR K 92 ARG 0.006 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 80) hydrogen bonds : angle 5.20282 ( 204) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.93227 ( 10) covalent geometry : bond 0.00283 ( 3237) covalent geometry : angle 0.59575 ( 4394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8257 (m-30) cc_final: 0.7960 (m-30) REVERT: A 474 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7377 (tm-30) REVERT: H 47 TRP cc_start: 0.8954 (t60) cc_final: 0.8583 (t60) REVERT: H 57 ASN cc_start: 0.8348 (t0) cc_final: 0.8038 (t0) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.2053 time to fit residues: 18.5791 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101843 restraints weight = 6753.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102496 restraints weight = 5697.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103539 restraints weight = 5842.871| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3242 Z= 0.174 Angle : 0.625 7.965 4404 Z= 0.329 Chirality : 0.044 0.139 467 Planarity : 0.004 0.036 569 Dihedral : 5.054 24.507 447 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.79 % Allowed : 17.20 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.41), residues: 392 helix: -4.28 (0.81), residues: 15 sheet: -0.83 (0.45), residues: 125 loop : -1.21 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.016 0.002 PHE K 84 TYR 0.021 0.002 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 80) hydrogen bonds : angle 5.07096 ( 204) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.97630 ( 10) covalent geometry : bond 0.00415 ( 3237) covalent geometry : angle 0.62437 ( 4394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8301 (m-30) cc_final: 0.7951 (m-30) REVERT: A 474 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7558 (tm-30) REVERT: H 57 ASN cc_start: 0.8388 (t0) cc_final: 0.8132 (t0) REVERT: K 61 ASP cc_start: 0.7306 (t0) cc_final: 0.7016 (t0) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.2019 time to fit residues: 18.5188 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102536 restraints weight = 6593.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102691 restraints weight = 5621.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103909 restraints weight = 5769.886| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3242 Z= 0.144 Angle : 0.646 8.562 4404 Z= 0.336 Chirality : 0.043 0.131 467 Planarity : 0.004 0.038 569 Dihedral : 4.986 24.840 447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.21 % Allowed : 17.78 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.41), residues: 392 helix: -4.35 (0.75), residues: 15 sheet: -0.82 (0.45), residues: 129 loop : -1.15 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.007 0.001 PHE A 400 TYR 0.017 0.002 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 80) hydrogen bonds : angle 4.93744 ( 204) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.63147 ( 10) covalent geometry : bond 0.00345 ( 3237) covalent geometry : angle 0.64184 ( 4394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8295 (m-30) cc_final: 0.7949 (m-30) REVERT: A 474 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 57 ASN cc_start: 0.8336 (t0) cc_final: 0.8116 (t0) REVERT: K 61 ASP cc_start: 0.7383 (t0) cc_final: 0.7056 (t0) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.2119 time to fit residues: 19.4347 Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101931 restraints weight = 6548.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102057 restraints weight = 5090.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102717 restraints weight = 5009.277| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3242 Z= 0.146 Angle : 0.635 8.085 4404 Z= 0.333 Chirality : 0.043 0.131 467 Planarity : 0.005 0.057 569 Dihedral : 4.828 23.548 447 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.62 % Allowed : 17.20 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.41), residues: 392 helix: -4.36 (0.75), residues: 15 sheet: -0.83 (0.44), residues: 135 loop : -1.12 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 392 TYR 0.016 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 80) hydrogen bonds : angle 4.86260 ( 204) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.32528 ( 10) covalent geometry : bond 0.00345 ( 3237) covalent geometry : angle 0.63224 ( 4394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7654 (m-10) cc_final: 0.7406 (m-10) REVERT: A 474 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7597 (tm-30) REVERT: H 57 ASN cc_start: 0.8332 (t0) cc_final: 0.8116 (t0) REVERT: K 61 ASP cc_start: 0.7447 (t0) cc_final: 0.7144 (t0) outliers start: 9 outliers final: 9 residues processed: 76 average time/residue: 0.2097 time to fit residues: 18.4495 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103346 restraints weight = 6588.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103211 restraints weight = 5246.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104619 restraints weight = 5188.856| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3242 Z= 0.136 Angle : 0.631 7.721 4404 Z= 0.332 Chirality : 0.043 0.129 467 Planarity : 0.004 0.037 569 Dihedral : 4.783 22.630 447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.92 % Allowed : 17.78 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.41), residues: 392 helix: -4.23 (0.86), residues: 15 sheet: -0.54 (0.45), residues: 133 loop : -1.10 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.007 0.001 PHE K 84 TYR 0.015 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02800 ( 80) hydrogen bonds : angle 4.74043 ( 204) SS BOND : bond 0.00225 ( 5) SS BOND : angle 1.22382 ( 10) covalent geometry : bond 0.00322 ( 3237) covalent geometry : angle 0.62855 ( 4394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7624 (m-10) cc_final: 0.7372 (m-10) REVERT: A 405 ASP cc_start: 0.8356 (m-30) cc_final: 0.8105 (m-30) REVERT: A 474 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7558 (tm-30) REVERT: H 57 ASN cc_start: 0.8316 (t0) cc_final: 0.8110 (t0) REVERT: K 39 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: K 61 ASP cc_start: 0.7517 (t0) cc_final: 0.7198 (t0) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.2193 time to fit residues: 18.8043 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102577 restraints weight = 6570.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102273 restraints weight = 5641.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103513 restraints weight = 6108.265| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3242 Z= 0.153 Angle : 0.638 7.572 4404 Z= 0.338 Chirality : 0.044 0.132 467 Planarity : 0.005 0.038 569 Dihedral : 4.863 22.578 447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.79 % Allowed : 17.49 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.42), residues: 392 helix: -3.79 (0.90), residues: 21 sheet: -0.47 (0.46), residues: 133 loop : -1.12 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 400 TYR 0.016 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 80) hydrogen bonds : angle 4.73500 ( 204) SS BOND : bond 0.00229 ( 5) SS BOND : angle 1.15732 ( 10) covalent geometry : bond 0.00365 ( 3237) covalent geometry : angle 0.63662 ( 4394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7666 (m-10) cc_final: 0.7460 (m-10) REVERT: A 405 ASP cc_start: 0.8303 (m-30) cc_final: 0.8064 (m-30) REVERT: A 474 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7581 (tm-30) REVERT: H 57 ASN cc_start: 0.8328 (t0) cc_final: 0.8102 (t0) REVERT: K 61 ASP cc_start: 0.7469 (t0) cc_final: 0.7161 (t0) REVERT: K 82 GLU cc_start: 0.8061 (pm20) cc_final: 0.7808 (pm20) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2013 time to fit residues: 17.0915 Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102834 restraints weight = 6648.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102470 restraints weight = 5509.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104233 restraints weight = 5239.445| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3242 Z= 0.151 Angle : 0.636 7.379 4404 Z= 0.336 Chirality : 0.043 0.138 467 Planarity : 0.004 0.035 569 Dihedral : 4.812 22.502 447 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.50 % Allowed : 18.37 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.42), residues: 392 helix: -3.83 (0.89), residues: 21 sheet: -0.42 (0.46), residues: 133 loop : -1.12 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 400 TYR 0.016 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 80) hydrogen bonds : angle 4.65654 ( 204) SS BOND : bond 0.00247 ( 5) SS BOND : angle 1.13743 ( 10) covalent geometry : bond 0.00361 ( 3237) covalent geometry : angle 0.63473 ( 4394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.02 seconds wall clock time: 28 minutes 24.28 seconds (1704.28 seconds total)